If you are using CanIt-Domain-PRO or Hosted CanIt and all the domains you wish to delete are in their own realm, just delete the realm under Setup->Realms. Remember that you cannot delete the realm you're currently viewing. It's best to switch into the parent of the realm you wish to delete.
If you are using CanIt-PRO or the domains to be deleted are in a realm with other domains you want to keep, then you need to delete the domains' entries under:
Setup->Verification Servers Setup->Domain Mappings Setup->Authentication Mappings Setup->Domain Routing Setup->Realm Mappings (not applicable for CanIt-PRO)
Be sure to delete the domain from Setup->Realm Mappings last, because that makes you relinquish control of the domain completely.